Zanivan 2023

 Prof Sara Zanivan

Head of Proteomics Facility

The Advanced Technology Proteomic Facility develops MS-based platforms and works together with researchers to provide a new level of understanding in tumour biology. We have developed pipelines for the analysis of a wide range of biological samples, from single proteins to the complete proteome of cells, organoids and tissues.

Our group has recently developed new methods to study cysteine oxidation (van der Reest, Lilla et al. Nature Communications 2018), cell secretomes (Hernandez-Fernaud, Ruengeler et al. Nature Communications 2017) and transmembrane receptor trafficking (Diaz-Vera et al. Journal Cell Science 2017).

We have three MS instruments, each coupled to an Easy-nLC system:

  • Orbitrap Fusion Lumos
  • Q-Exactive HF
  • LTQ Orbitrap Elite

We use a variety of methods for protein digestion:

  • filter-aided sample preparation (FASP)
  • in-gel
  • in-solution

for proteome and post-translational modifications analysis:

  • high-pH reversed-phase chromatography peptide fractionation
  • gel-based protein fractionation

to accurately measure proteins and peptides:

  • Label-free
  • TMT
  • Dimethyl
  • Isotope-labelled IAA (for cysteine oxidation)

We analyse our MS data with

  • MaxQuant computational platform
  • Progenesis and Skyline for the analysis of pRM data
  • Mascot for single protein identification
  • Perseus and Scaffold for data compilation, analysis and dissemination.

Sara Zanivan also leads the Tumour Microenvironment and Proteomics research group.